BioCyc database collection


A comprehensive website for sharing fundamental information about biochemical pathways and genomes with researchers around the world.

The BioCyc database collection is a set of more than 9,300 Pathway/Genome Databases (PGDBs) describing many sequenced genomes. The comprehensive website enables researchers around the world to share fundamental information about biochemical pathways and genomes.

PGDBs describe the entire genome of an organism, as well as its biochemical pathways and (when curated) its regulatory network. All PGDBs are structured within a rich ontology that supports computational exploration. BioCyc supports activities in drug discovery, agriculture, and biotechnology by enhancing the understanding of biological systems.

The BioCyc website contains many tools for navigating and analyzing these databases, and for analyzing omics data, including:

  • Genome browser
  • Display of individual metabolic pathways, and of full metabolic maps
  • Visual analysis of user-supplied omics datasets by painting onto metabolic map, regulatory map, and genome map
  • Comparative analysis tools

New expanded versions of BioCyc are released three times per year.

The downloadable version of BioCyc that includes SRI’s Pathway Tools software provides more speed and power than the BioCyc website. Pathway Tools can also be installed locally to create BioCyc-like databases for additional organisms. The software is available for license to academic and commercial groups.

PGDBs in the BioCyc collection include:

  • EcoCyc: This Escherichia coli K-12 database was compiled through literature-based curation of almost 32,000 articles. EcoCyc provides mini-review summaries of 3,300 E. coli genes, and descriptions of the metabolic and transcriptional regulatory networks of E. coli.
  • HumanCyc: A unique collection of human metabolic pathway data derived from computational pathway analysis of the human genome and literature-based curation.
  • MetaCyc: Describes more than 2,500 metabolic pathways and more than 14,000 reactions  from more than 2,800 organisms. MetaCyc data and commentary
    were gathered from more than 52,000 publications to provide a comprehensive metabolic encyclopedia, particularly for microbial and plant metabolism.

The NIH National Institute for General Medical Sciences funds development of the MetaCyc database and the BioCyc collection under grant GM080746. The NIH National Institute for General Medical Sciences and National Center for Research Resources co-fund development of the EcoCyc database under grant GM077678. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.

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